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1.
J Chem Phys ; 150(4): 044107, 2019 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-30709286

RESUMO

Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a kernel-based pipeline that can learn and predict the atomization energy of molecules with high accuracy. The framework employs Gaussian process regression to perform predictions based on the similarity between molecules, which is computed using the marginalized graph kernel. To apply the marginalized graph kernel, a spatial adjacency rule is first employed to convert molecules into graphs whose vertices and edges are labeled by elements and interatomic distances, respectively. We then derive formulas for the efficient evaluation of the kernel. Specific functional components for the marginalized graph kernel are proposed, while the effects of the associated hyperparameters on accuracy and predictive confidence are examined. We show that the graph kernel is particularly suitable for predicting extensive properties because its convolutional structure coincides with that of the covariance formula between sums of random variables. Using an active learning procedure, we demonstrate that the proposed method can achieve a mean absolute error of 0.62 ± 0.01 kcal/mol using as few as 2000 training samples on the QM7 dataset.

2.
J Chem Phys ; 148(3): 034101, 2018 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-29352799

RESUMO

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

3.
Comput Phys Commun ; 217: 171-179, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29104303

RESUMO

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

4.
Biophys J ; 112(10): 2030-2037, 2017 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-28538143

RESUMO

We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment-simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles-using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e., a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and the shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood cells.


Assuntos
Eritrócitos/metabolismo , Simulação de Dinâmica Molecular , Software , Algoritmos , Animais , Membrana Celular/metabolismo , Análise por Conglomerados , Citoesqueleto/metabolismo , Eritrócitos/citologia , Modelos Cardiovasculares
5.
Phys Rev E ; 93(3): 033312, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-27078489

RESUMO

We analyze hydrodynamic fluctuations of a hybrid simulation under shear flow. The hybrid simulation is based on the Navier-Stokes (NS) equations on one domain and dissipative particle dynamics (DPD) on the other. The two domains overlap, and there is an artificial boundary for each one within the overlapping region. To impose the artificial boundary of the NS solver, a simple spatial-temporal averaging is performed on the DPD simulation. In the artificial boundary of the particle simulation, four popular strategies of constraint dynamics are implemented, namely the Maxwell buffer [Hadjiconstantinou and Patera, Int. J. Mod. Phys. C 08, 967 (1997)], the relaxation dynamics [O'Connell and Thompson, Phys. Rev. E 52, R5792 (1995)], the least constraint dynamics [Nie et al.,J. Fluid Mech. 500, 55 (2004); Werder et al., J. Comput. Phys. 205, 373 (2005)], and the flux imposition [Flekkøy et al., Europhys. Lett. 52, 271 (2000)], to achieve a target mean value given by the NS solver. Going beyond the mean flow field of the hybrid simulations, we investigate the hydrodynamic fluctuations in the DPD domain. Toward that end, we calculate the transversal autocorrelation functions of the fluctuating variables in k space to evaluate the generation, transport, and dissipation of fluctuations in the presence of a hybrid interface. We quantify the unavoidable errors in the fluctuations, due to both the truncation of the domain and the constraint dynamics performed in the artificial boundary. Furthermore, we compare the four methods of constraint dynamics and demonstrate how to reduce the errors in fluctuations. The analysis and findings of this work are directly applicable to other hybrid simulations of fluid flow with thermal fluctuations.

6.
Interface Focus ; 6(1): 20150065, 2016 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-26855752

RESUMO

Sickle-cell anaemia (SCA) is an inherited blood disorder exhibiting heterogeneous cell morphology and abnormal rheology, especially under hypoxic conditions. By using a multiscale red blood cell (RBC) model with parameters derived from patient-specific data, we present a mesoscopic computational study of the haemodynamic and rheological characteristics of blood from SCA patients with hydroxyurea (HU) treatment (on-HU) and those without HU treatment (off-HU). We determine the shear viscosity of blood in health as well as in different states of disease. Our results suggest that treatment with HU improves or worsens the rheological characteristics of blood in SCA depending on the degree of hypoxia. However, on-HU groups always have higher levels of haematocrit-to-viscosity ratio (HVR) than off-HU groups, indicating that HU can indeed improve the oxygen transport potential of blood. Our patient-specific computational simulations suggest that the HVR level, rather than the shear viscosity of sickle RBC suspensions, may be a more reliable indicator in assessing the response to HU treatment.

7.
BMC Genomics ; 17 Suppl 1: 4, 2016 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-26818118

RESUMO

BACKGROUND: The identification of inversions of DNA segments shorter than read length (e.g., 100 bp), defined as micro-inversions (MIs), remains challenging for next-generation sequencing reads. It is acknowledged that MIs are important genomic variation and may play roles in causing genetic disease. However, current alignment methods are generally insensitive to detect MIs. Here we develop a novel tool, MID (Micro-Inversion Detector), to identify MIs in human genomes using next-generation sequencing reads. RESULTS: The algorithm of MID is designed based on a dynamic programming path-finding approach. What makes MID different from other variant detection tools is that MID can handle small MIs and multiple breakpoints within an unmapped read. Moreover, MID improves reliability in low coverage data by integrating multiple samples. Our evaluation demonstrated that MID outperforms Gustaf, which can currently detect inversions from 30 bp to 500 bp. CONCLUSIONS: To our knowledge, MID is the first method that can efficiently and reliably identify MIs from unmapped short next-generation sequencing reads. MID is reliable on low coverage data, which is suitable for large-scale projects such as the 1000 Genomes Project (1KGP). MID identified previously unknown MIs from the 1KGP that overlap with genes and regulatory elements in the human genome. We also identified MIs in cancer cell lines from Cancer Cell Line Encyclopedia (CCLE). Therefore our tool is expected to be useful to improve the study of MIs as a type of genetic variant in the human genome. The source code can be downloaded from: http://cqb.pku.edu.cn/ZhuLab/MID .


Assuntos
Algoritmos , Inversão Cromossômica/genética , Sequenciamento de Nucleotídeos em Larga Escala , DNA/química , DNA/genética , DNA/metabolismo , Genoma Humano , Humanos , Internet , Alinhamento de Sequência , Análise de Sequência de DNA , Interface Usuário-Computador
8.
Chem Commun (Camb) ; 51(55): 11038-40, 2015 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-26062446

RESUMO

We present a non-isothermal mesoscopic model for investigation of the phase transition dynamics of thermoresponsive polymers. Since this model conserves energy in the simulations, it is able to correctly capture not only the transient behavior of polymer precipitation from solvent, but also the energy variation associated with the phase transition process. Simulations provide dynamic details of the thermally induced phase transition and confirm two different mechanisms dominating the phase transition dynamics. A shift of endothermic peak with concentration is observed and the underlying mechanism is explored.


Assuntos
Transição de Fase , Polímeros/química , Modelos Moleculares , Termodinâmica
9.
Chem Commun (Camb) ; 50(61): 8306-8, 2014 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-24938634

RESUMO

We present large-scale simulation results on the self-assembly of amphiphilic systems in bulk solution and under soft confinement. Self-assembled unilamellar and multilamellar vesicles are formed from amphiphilic molecules in bulk solution. The system is simulated by placing amphiphilic molecules inside large unilamellar vesicles (LUVs) and the dynamic soft confinement-induced self-assembled vesicles are investigated. Moreover, the self-assembly of sickle hemoglobin (HbS) is simulated in a crowded and fluctuating intracellular space and our results demonstrate that the HbS self-assembles into polymer fibers causing the LUV shape to be distorted.


Assuntos
Lipossomas Unilamelares/química , Eritrócitos/química , Eritrócitos/fisiologia , Hemoglobina Falciforme/química , Hemoglobina Falciforme/metabolismo , Humanos , Interações Hidrofóbicas e Hidrofílicas , Lipossomas Unilamelares/metabolismo
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